The turbulent internal politics of Iran following the June 12 election have been most often portrayed as a clash between secularizing reform forces and entrenched religious forces. However, this is a mischaracterization. The controversy is fundamentally between two very old, very entrenched religious philosophies that have been debated for more than 300 years. It's a debate at the heart of every major political uprising in the nation's history from that time forward. Even if the present controversy is quelled, this debate will continue for the immediate future, likely resulting in a major governmental shift.

The fundamental debate is over the role of religion in the governance of the state. The Safavid Dynasty, founded in the 17th Century, marks the beginning of modern Iran. The Safavids were an Azerbaijani Turkish Shi'a Muslim religious order with strong ties to Sufi mysticism. They eventually conquered the Caucasus, Central Asia and Northern India.

From the very beginning the question of the role of religion in the state was a great issue. The Safavids established "Twelver" Shi'a Islam as the state religion, and from that time forward most of the institutions of modern Shi'ism were established. This included the doctrine that all Shi'a believers should choose a "person worthy of emulation" to serve as their spiritual guide. Eventually, these "Marjeh-ye Taqlid" were recognized as Grand Ayatollahs, renowned for their scholarship, which was established in a "thesis" that included their views of Islamic laws. They also believed that the Twelfth Imam after the Prophet Mohammad, called the "Mahdi," had vanished in the Golden Mosque in Samarra and would eventually return at the end of time, with Jesus, to render the final judgment of humankind. The Mahdi remains for modern Shi'a believers the ultimate true authority.

The wisest religious scholars warned the Safavids that Islamic clerics should not get involved with government, lest they become corrupt. They pointed out that Islam says very little about statecraft or the formation of governmental institutions and that the compromises of politics are often incompatible with religious piety.

The Safavids didn't listen. They became powerful and eventually did become corrupt, until they were weakened and conquered by forces from Afghanistan. Another Turkish Dynasty, the Qajars, arose in the 19th Century, with the same fundamental problems of reconciling religious institutions with the State. The Qajar shahs were often at odds with the clergy—particularly when they began to meet the economic and military challenges of Europe by selling "concessions" to Europeans for the exploitation of Iran's natural resources and economic institutions. The result was an Islamic backlash with open rebellion against the state that launched the modern Islamic movement and led to Iran's first constitution in 1905.

Toward the end of the Qajar period, prominent Islamic scholars Shaykh Fazollah Nuri and Ayatollah Mohammad Hossein Na'ini maintained opposite viewpoints about the role of clerics in government. As Iran scholar Abbas Milani pointed out in a July 15 article in The New Republic, Sheikh Nuri believed that, in the absence of the hidden Mahdi, religious clerics had ultimate authority in the modern state, and could veto legislation if it was not sufficiently Islamic.

Ayatollah Na'ini asserted that no human government could substitute for the true "Islamic government" to be established by the Mahdi at his return. In the interim, humans had to do the best they could. For Na'ini, this was a constitutional democracy in which, according to Milani, "The role of ayatollahs . . . would be to "advise" the rulers and ensure that laws inimical to sharia were not implemented. But it would not be to rule the country themselves." Na'ini approved the establishment of the Pahlavi dynasty, which ruled Iran until the Islamic Revolution of 1979.

Ayatollah Ruhollah Khomeini, who lead the Islamic Revolution which deposed the shah, at first seemed to embrace Na'ini's philosophy of clerical non-involvement. After the revolution succeeded, however, he reversed course, and embraced Nuri's philosophy, to the consternation of the majority of the Grand Ayatollahs. The Iranian constitution, consequently, rests on the principle of the "Velayat-e Faqih," or the "Regency of the Chief Jurisprudent," in which a senior scholar is chosen as Regent for the absent Mahdi. This is Iran's "Supreme Leader" today.

Clerics who opposed this doctrine at the time were stripped of their credentials, and some were placed under house arrest.

When Ayatollah Khomeini died, it was difficult to find a successor who would take on the role of Supreme Leader. Ali Khamene'i was finally chosen. He was not a cleric of the first rank, but he was quickly elevated to the rank of Ayatollah. His legitimacy was questioned from the moment he took office.

The controversy still rages. Ayatollah Mohammad-Taqi Mesbah-Yazdi, one of the most conservative clerics in the holy shrine city of Qom, and spiritual advisor to President Ahmadinejad, is a supporter of the Nuri position. He has declared that elections are unnecessary now that proper Islamic rule is in place. He reportedly told election workers before the June 12 election that it would be permissible for them to fix the election to make sure that Ahmadinejad could continue in office to support religious rule.

Ahmadinejad's chief rival, Mir Hossein Mousavi, is no less pious, but he espouses the religious philosophy embodied in the writings of Ayatollah Na'ini—that a secular democracy should be the basic form of government for Iran, with religious scholars serving merely as advisors.

This is also the position favored by the most influential Grand Ayatollah in Iraq, Ayatollah Ali al-Sistani of Najaf. Some of the most revered clerics in Iran have likewise denounced the election, thus tacitly revealing their opposition to the principle of the Supreme Leader.

The current attacks questioning the election are thus seen by both Ahmadinejad and Ayatollah Khamene'i as attacks against the most fundamental principle of the current constitution of the Islamic Republic. If the reformers prevail, the constitution would likely be rewritten, and the office of Supreme Leader would be eliminated or greatly reduced in influence. This was threatening not only to the two top office holders, but to everyone else whose power depended on them, including the Revolutionary Guard, and the Basij militia forces, both of which were established to "guard the principles of the Revolution."

Even if the current controversy dies down, and Ahmadinejad assumes a second presidential term, the crisis will continue. Supreme Leader Khamene'i has no obvious successor, and with the majority of Grand Ayatollahs opposing the very existence of the office, it is unclear who will be found to fill it.

William O. Beeman is professor and chair of the Department of Anthropology at the University of Minnesota. He has conducted research on Iran for more than 30 years and lived through the Revolution of 1978-79. He is the author of The "Great Satan" vs. the "Mad Mullahs": How the United States and Iran Demonize Each Other.